Which Tm should I use in figuring out the annealing temperature in Quik-change site-directed mutagenesis, the basic or salt adjusted Tm?

It is recommended to use the salt adjusted Tm. On our OligoAnalyzer SciTool there is also an option to analyze the Tm of the sequence with mismatched base. Enter the sequence then click on mismatch. You will have an option to change as many bases as you wish per sequence by clicking on the base and then choosing the base you wish to have inserted instead of the exact match. When you click calculate, it will give information on the exact and mismatch Tms.